Effects of flanking G.cntdot.C base pairs on internal Watson-Crick, G.cntdot.U and nonbonded base pairs within a short RNA duplex

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Abstract
A series of pentaribonucleotides, ApGpXpGpU (where X.tbd. A, G, C or U), was synthesized to investigate the effects of flanking G.cntdot.C pairs on internal Watson-Crick, G.cntdot.U, and nonbonded base pairs. Sequences ApGpApCpU (Tm [melting temperature] = 26.degree. C) and ApGpCpCpU (Tm = 25.degree. C) were each found to form a duplex with non-base-paired internal residues that stacked with the rest of the sequence but were not looped out. ApGpGpCpU also forms a duplex (Tm = 30.degree. C) but with dangling terminal nonbonded adenosines rather than internal nonbonded guanosines. ApGpUpCpU prefers a stacked single-strand conformation. In addition, contribution to duplex stability from an internal A.cntdot.U or G.cntdot.C base pair is enhanced by 6.degree. C when flanked by G.cntdot.C base pair as compared to A.cntdot.U base pairs. G.cntdot.C base pairs flanking an internal G.cntdot.U base pair were more tolerant to the altered conformation of a G.cntdot.U pair and result in an increase to stability comparable with that found for an internal A.cntdot.U base pair.
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